Biology subjects

Fagernas, Z.

Publications and source records attributed to Fagernas, Z..

3 recordsLinked to original sources

bioRxiv2026

Beyond dairy: Identification of dental enamel proteins in ancient human dental calculus

Ancient human dental calculus is one of the richest archives of archaeological biomolecular information, providing direct evidence of diet, oral health, and the oral microbiome. Proteomic analyses of this biological matrix have so far focused mainly on oral microbes and dietary proteins, with milk proteins such as beta-lactoglobulin (BLG) providing the largest corpus of proteomic evidence. Despite the close relation between the various stages of dental calculus formation and mineralization with the dental enamel surface, proteins from the dental enamel matrix have not previously been reported outside of dental enamel tissue. Here we reanalysed 498 ancient dental calculus proteomes from 14 published studies (n=434 individuals) reporting the presence of BLG, spanning from the Neolithic to the Victorian Era and applying different protein extraction protocols (FASP, GASP, SP3 and in-solution digestion). Dental enamel matrix proteins were identified in ten studies (n=37 individuals), with amelogenin being the most frequently detected. Enamel peptides occurred more often in studies that applied SP3, although amelogenin was successfully identified through both SP3 and FASP. Structural proteins, including enamelin, ameloblastin, and MMP20, were also identified. The detection of AMELX and AMELY peptide sequences provided new insights into cases where the sex was previously undetermined. These findings establish dental enamel proteins as a new category of biomolecules detected in dental calculus, broadening its application beyond diet and microbiome studies to possible sex estimation. HighlightsO_LIDental calculus entraps oral microbes along with endogenous and exogenous particles during formation and mineralization C_LIO_LIWe conduct reanalysis of 14 published ancient dental calculus studies (n = 434 individuals) spanning the Neolithic to Victorian Era C_LIO_LIDental enamel proteins AMELX, AMELY, AMBN, COL17A1, ENAM and MMP20 are identified in ancient human dental calculus C_LIO_LIAmelogenin was the most frequently detected enamel protein C_LIO_LIWe expand dental calculus palaeoproteomics beyond diet and oral microbiome to potentially include sex estimation C_LI

evolutionary biology↗

bioRxiv2023

Exploring archaeogenetic studies of dental calculus to shed light on past human migrations in Oceania

The Pacific islands have experienced multiple waves of human migrations, providing a case study for exploring the potential of using the microbiome to study human migration. We performed a metagenomic study of archaeological dental calculus from 103 ancient individuals, originating from 12 Pacific islands and spanning a time range of [~]3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone from the Pacific, and comparable to that seen in calculus from temperate regions. Variation in the microbial community composition was minimally driven by time period and geography within the Pacific, while comparison with samples from Europe, Africa, and Asia reveal the microbial communities of Pacific calculus samples to be distinctive. Phylogenies of individual bacterial species in Pacific calculus reflect geography. Archaeological dental calculus shows potential to yield information about past human migrations, complementing studies of the human genome.

microbiology↗

bioRxiv2023

Assessing the validity of a calcifying oral biofilm model as a suitable proxy for dental calculus

AO_SCPLOWBSTRACTC_SCPLOWDental calculus is increasingly used by researchers to study dietary patterns in past populations. The benefits of using dental calculus for this purpose have been clearly demonstrated in previous studies, with dental calculus harbouring a wealth of microremains and biomarkers for health and diet within its mineral matrix. Previous studies have demonstrated some of the limitations and biases of how methods of processing may overlook, or even remove, some of the important information contained within the mineralised matrix. However, there are many factors that are impossible to account for in vivo and in archaeological material, such as exact dietary intake, and individual factors such as pH and enzyme activity, leaving some limitations that may not be addressed through these types of studies and will require a different approach. We present a protocol for creating a calcifying oral biofilm model that can be used to explore the biases and limitations of dental calculus as a medium for paleodietary reconstructions. We report the microbial and mineral composition of our model in an effort to validate the model calculus as an appropriate proxy to natural dental calculus. The microbial profile and species diversity of our model was determined using metagenomic classification with the nf-core/eager pipeline and Kraken2, and compared to various reference samples from oral sites, including saliva, plaque, and dental calculus. We then assessed whether our model calculus mineralises in a manner similar to natural dental calculus using Fourier transform infrared (FTIR) spectroscopy. The metagenomic classification showed a microbial profile predominantly made up of (facultative) anaerobes, with a community structure that was somewhat distinct from other oral reference samples. The core genera of the model consisted of oral species, but clustered separately from oral reference samples, with a higher abundance of anaerobes. Mineral and organic components of our model mimic that of the modern and archaeological reference calculus that was used as a comparison. There was an overall increase in the inorganic component relative to organic over the course of the experiment, with carbonated hydroxyapatite as the principal compound, consistent with natural human-derived calculus. We conclude that oral biofilm models, such as the one presented in this study, have great potential to validate current methods used in the analysis of archaeological dental calculus, and should be used to complement, rather than replace current in vivo studies.

microbiology↗